Scientists have reconstructed the whole genetic code, or genome, of a group of ancient humans called Denisovans. They interbred with our species and the DNA results suggest they had dark hair, eyes, and skin, the journal Science reports.

In 2010, scientists from the Max Planck Institute in Germany announced the new human group based on DNA evidence from a finger bone fossil found in Denisova Cave in the Altai Mountains, Siberia.

That first DNA was obtained from mitochondria, tiny power structures in each human cell that contain their own DNA. Now, many of the same team have used a new approach and have sequenced chromosomal DNA (the DNA of the cell nucleus which contains most genes) from the same finger bone fossil.

'They were able to reconstruct the whole genome to a quality matching that obtained for living humans,' says Professor Chris Stringer, human origins expert at the Natural History Museum.

'The higher quality genome not only provides greater confidence about previous conclusions, but also adds many details about the Denisovans, and how modern humans may have differed from them,' adds Stringer.

Skull of Homo heidelbergensis, the ancient human species that may be the ancestor of the mystery Denisovan human.

'The research confirms that the Denisovans were related to the Neanderthals, and that many present-day Australasians have Denisovan DNA from an ancient interbreeding event.'

Some theories place Denisovans, along with Neanderthals and modern humans, as the descendents of the ancient human Homo heidelbergensis who lived about 500,000 years ago.

Potential biological differences

By comparing the genomes of Denisovans, apes, Neanderthals and different modern human populations, the team could identify DNA segments unique to these different groups.

This may help shed light on potential biological differences between modern humans and the Neanderthal and Denisovan populations they replaced, Stringer says.

For example, in modern humans, unique segments were associated with brain function and nervous system development, as well as diseases affecting the skin and eyes.

'Perhaps some of the skin and eye-related ones reflect resistance to diseases in the African homeland of modern humans, but the brain-related ones hint at possible enhancements in brain structure and function in our species.'

Two Neanderthal interbreeding events?

Skull of a Neanderthal, Homo neanderthalensis

The Denisovan genome also reveals more clues about Denisovan and Neanderthal interbreeding with modern humans. Until now, evidence suggested that after modern humans dispersed from Africa about 60,000 years ago, there was a single interbreeding event with Neanderthals.

'Previous research suggested that all recent populations originating from outside of Africa had received about the same amount of Neanderthal input, implying a single early hybridisation event somewhere like the Middle East,' says Stringer.

However, the results of this study show that the Neanderthal genetic input to modern human populations outside of Africa varies. 'This suggests that, overall, Europeans have less Neanderthal DNA (about 1%) than populations to the east (1.7%),' explains Stringer.

'This might imply changes in the proportions after interbreeding took place, or that there was more than one interbreeding event.'

Denisovan interbreeding confirmation

The team found that the Denisovan genetic input in Australasian populations averaged about 3%. 'This supports the idea that Denisovans must have been present in south east Asia, where the hypothesised interbreeding with the ancestors of present-day Australasians occurred, as well as in Siberia,' says Stringer.

Low genetic diversity

Our genes often come in different variants, such as those for skin colour or eye colour and a large population will generally hold more variation than a small population. But, the Denisovan DNA results showed very low diversity, much less than a single modern human would show, says Stringer.

'This is surprising because the previous mitochondrial DNA research had suggested relatively high diversity, and interbreeding with the ancestors of Australasians (who are thought to have passed through southern Asia rather than Siberia) implied that the Denisovans were widespread in Asia, also leading to the expectation of a large and diverse population.'

'The surprisingly low genetic diversity of the Denisovans may indicate, as with Neanderthals to the west, that the core territory of the Denisovans was well to the south, and that they only expanded to regions like the Altai during brief warm intervals, and in small numbers.'

Other physical features

Apart from the genetic evidence of a dark complexion, Stringer says we need to find out more about what the Denisovans looked like physically. 'This will require the recovery of ancient DNA from more complete fossils, perhaps in Denisova Cave itself, or from specimens in regions like China,’ he says.

'The genome does not tell us how big their brains or brow ridges were, if they had chins, or how tall and robust they were. Hence we need to have Denisovan DNA from more complete fossils to link the genome to morphology'.

Function of shared DNA

Stringer says that further research should also help explain what function, if any, the Denisovan and Neanderthal DNA has in the modern humans that hold it.

More interbreeding

Finally, there is an issue that perhaps cannot be addressed properly until higher quality reconstructions of Neanderthal genomes also become available, says Stringer. If modern humans interbred successfully with both Neanderthals and Denisovans, did Neanderthals and Denisovans interbreed?

Stringer thinks this is likely. 'It seems highly probable that they did, given that they co-existed in Eurasia for hundreds of millennia, and Denisova cave itself has evidence of Neanderthal DNA in a fossil foot bone.'

Stringer concludes, 'Recognition of such interbreeding will inevitably complicate the untangling of the relationships between these ancient groups of humans, and their contributions to people today.'